Just download the RAR, ZIP, 7ZIP or other format files to your PC.
Open them (uncompress) to any place in your PC. Once you do that, check the file structure of the folder you just extracted, it should be something like this: MOD Name\Data\.....
Make sure that there is not another "MOD Name" folder inside the first one... this happens sometimes. If this is the case, make sure there is only one.
Once you have it as I first explained, copy it to your MODS folder located in your SilentHunterIII directory. Now you can close the window.
Click on the JSGME icon and you should see the folder you just copied at the left side of the window. Select it with one click and hit the ">" button..... Voilá, you just enabled the mod!!!
I hope this helped you... if you have more questions, just ask.
CapZap